5 Answers

>Alakazam's brain continually grows, infinitely multiplying brain cells. This amazing brain gives this Pokémon an astoundingly high IQ of 5,000. It has a thorough memory of everything that has occurred in the world.

>One of the world's smartest computers took an intelligence test and scored as well as a four-year-old human being.

Further,

>The computer basically can name the dots, but can't connect them.

From here on, it seems simpler. Basically, Metagross can solve equations, but not necessarily understand them, or know them. On the other hand, Alakazam has the ability to know and remember everything in the world. Implying that not only does it know the equation that Metagross solves within seconds, but also why, and the answer, kind of before hand. Also, the Dex entry talks of infinite brain-cell generating capabilities, that, in my opinion, out-trumps Metagross without a doubt.

Also, Metagross can only analyze, meaning it would probably fail the Turing test (keep in mind, however, it does use this in battles, so it is question of whether it is acting them out as simulations, or as actual strategies. If they are merely simulations, then it is not AI, but given that it acts based on the simulations, it may be AI). Now, Alakazam, as we know, has Intelligence of its own, and acts based on strategies it creates, as opposed to Metagross, instead of creating simulations, and discarding those that aren't beneficial.

How kind of you to say that, Astro! :3 (No seriously, you made my day!)

Well, about Uxie, it IS legendary Pokemon created SPECIFICALLY to represent Knowledge itself. If you think of it as an embodiment, or a rather, spirit, or entity, designed to keep things in check, as opposed to a Pokemon then indeed, Uxie can't be compared to either of the above Pokemon in terms of IQ.

And, Luke, no problem at all, man! I had fun thinking about the answer to this, and digging up stuff that I hadn't known previously either! It was a great question, one that forced me to think about super-computers and other stuff that Alan Turing was good at. As for the name, glad that you like it. It is, to be honest, a kind of a play on my actual name (or rather, its translation). + It sounds cool af. :3

As far as I know, Alakazam is the only Pokemon that has had their IQ stated. Alakazam's IQ is also probably the highest because it's IQ is said to be around/over 5,000. We also know Metagross is very smart because it's Pokedex entries say that it's four brains are able to calculate difficult problems faster than a supercomputer. It doesn't tell Metagross's exact IQ but it tells that it is very smart.
Pokemon that also (probably) have a high IQ (Maybe the highest)
Lapras: Some of Lapras's Pokedex entries state that it is highly intelligent and it can understand human speech.
>Its high intelligence enables it to understand human speech. It likes to ferry people on its back.

Uxie: Uxie is the being of knowledge, it is most likely very smart.
Arceus: Arceus is the god of Pokemon, God knows everything.
Mew: The ancestor of all Pokemon must be very smart.
Beldum & Metang: The pre-evolutions of Metagross, Metagross is smart so Metang & Beldum are most likely smart.
Abra & Kadabra: Same thing with Beldum & Metang, they are the pre evolutions of Alakazam
Slowking: Look at dex entries. (Thanks Astro!!)

Alakazam

Metagross Ruby entry: METAGROSS has four brains in total. Combined, the four brains can breeze through difficult calculations faster than a supercomputer. This POKéMON can float in the air by tucking in its four legs

>Alakazam Red and Blue entry: Its brain can outperform a supercomputer. Its intelligence quotient is said to be 5,000.

Ok so both outperform a Super computer. Intelligent, huh? The highest IQ in the world is 154. So 5000 is a lot. If each Metang's iq was 500, it couldn't beat Alakazam.

Thats only in the game so it would be fair. If they could do that, everyone would be using them! Maybe they could, but perhaps they have battling laws for that or something. The games are just pieces of coding.

The Christian God is all knowing but Pokemon theology seems to be a bit different. It probably more closely models eastern religions where gods are more limited to roles or represent a universal energy or something like that. In Pokemon theology arceus may be God and still not all knowing. Uxie still stands out though. But wisdom and intelligence can be argued as not the same.